The incident happened at Craigdhu Primary School around 12pm on Tuesday afternoon.
Pupils were escorted from the building and fire crews attended, although they left shortly afterwards.
East Dunbartonshire Council said the alarm was set off because of fumes from an outside contractor’s maching.
Ann Davie, depute chief executive for education, said: "A carbon monoxide alarm in the school's plant room - separate from the main school building - was activated earlier today. No alarms within the school were activated and no carbon monoxide fumes were present in classrooms or in areas used by pupils.
"A site investigation concluded that fumes from a contractor's machinery being used outside got into the plant room and activated its alarm.
"In line with emergency procedures, and as a precaution, the Headteacher sounded the fire alarm to ensure a quick and safe evacuation. This resulted in the Scottish Fire & Rescue Service (SFRS) attending.
"Officers from SFRS, the Council's Health & Safety Team and SGN carried out a full investigation with pupils and staff being allowed back into the school which was assessed as being safe.
"A full investigation will be carried out into the incident."